Applications of genome sequencing as a single platform for clinical constitutional genetic testing

Abstract

The number of human disease genes has dramatically increased over the past decade, largely fueled by ongoing advances in sequencing technologies. In parallel, the number of available clinical genetic tests has also increased, including the utilization of exome sequencing for undiagnosed diseases. Although most clinical sequencing tests have been centered on enrichment-based multigene panels and exome sequencing, the continued improvements in performance and throughput of genome sequencing suggest that this technology is emerging as a potential platform for routine clinical genetic testing. A notable advantage is a single workflow with the opportunity to reflexively interrogate content as clinically indicated; however, challenges with implementing routine clinical genome sequencing still remain. This review is centered on evaluating the applications of genome sequencing as a single platform for clinical constitutional genetic testing, including its potential utility for diagnostic testing, carrier screening, cytogenomic molecular karyotyping, prenatal testing, mitochondrial genome interrogation, and pharmacogenomic and polygenic risk score testing.

Keywords: Clinical genome sequencing; Genome sequencing applications; Long-read sequencing; Medical genomics; Short-read sequencing.

Figure 1

Illustration of germline genome architecture and sequencing accessibility, as represented by6 clinically significant genes. From top left to bottom right: ADAMTSL2 (NM_014694.4; geleophysic dysplasia), CYP2D6 (NM_000106.6; drug metabolism), IKBKG (NM_001099857.5; incontinentia pigmenti), KRT86 (NM_001320198.2; monilethrix), OTOA (NM_144672.4; sensorineural hearing loss), and STRC (NM_153700.2; sensorineural hearing loss) (GRCh38). From inner to outer circles: previously reported exon-level sequencing “dead zones” across the genome (lifted over to GRCh38 from GRCh37; black); enrichment-based short-read exome sequencing coverage (average 185.8× across all coding regions; red); short-read genome sequencing coverage (average 33.2× across all coding regions; dark blue); long-read HiFi genome sequencing coverage (average 27.5× across all coding regions; light blue); and gene transcripts (introns: light green; exons: dark green). Noncoding exons were excluded from transcript tracks. All sequencing data were acquired from publicly available GIAB/NIST reference material sample NA12878 (HG001), filtered with mapping and base quality scores greater than Q20, and Circos images generated using R package circlize.

Figure 2

Illustration of Mendelian disease genes and pharmacogenomic genes across the human genome (GRCh38). From inner to outer circles: genes defined by the US FDA Table of Pharmacogenetic Associations as having “supportive evidence for therapeutic management recommendations” (blue) and “potentially impacted”/ “pharmacokinetics only” (red); genes with CPIC evidence levels A, A/B, B (blue) and C, C/D, D (red); OMIM-defined recessive (light green), dominant (dark green), and X-linked (gray) disease genes with an established molecular etiology (phenotype mapping key: 3); and ClinGen-defined recessive (light green), dominant (dark green), and X-linked (gray) disease genes with “definitive” or “strong” evidence. All data were downloaded from primary sources and Circos images generated using R package circlize.

Figure 3

Illustration of structural variation across the human genome (GRCh38). From inner to outer circles: ClinGen genes and genomic regions with “sufficient” or “emerging” evidence curated as haploinsufficient (red) and triplosensitive (blue) and DGV Gold Standard deletions (red), duplications (blue), and “other” structural variants (as defined by DGV; light green) found in the general population. All data were downloaded from primary sources and Circos images generated using R package circlize.